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Full Discussion: Select distinct sequences from fasta file and list
Top Forums UNIX for Dummies Questions & Answers Select distinct sequences from fasta file and list Post 302918693 by Marion MPI on Thursday 25th of September 2014 05:19:35 AM
Old 09-25-2014
Hi
Many thanks for the quick reply.
I tried but the output looks like
Code:
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGFGFPSIKHEEKTR
SDACNALTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
GRVQRSDRRHTRSILEYQNAGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHDEKNT
GRVQRSDRRHTRSILEYQDAGAVSCVQIFS*NQRKTRHLVFDNIAQGFGFPSIKHEEKTR
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGFGFPSIKHEEKNT
GRVQRSDRRHTRSILEYQDTGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHEEKNT
GRVQRSDRRHTRSILEYQDTGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHEEKNH
SDACNDLTDAILEASLNIRTPEPSLAFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNALTDAILEASLNIRTPEPSLAFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHDEKN
SDACNALTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFRP*SMKKKT
SDACNALTDVILEASLNIRTPEPSLGFRYSPKINEKTRHLVFDNIAQGFGFPSIKRDEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHDEKN
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGFGFPSIKHEEKTR
GRVQRLTDAILEASLNIRTPEPSLAFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKNT

instead of
Code:
>H8V34IS02HC5PK_rframe3
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGF
GFPSIKHEEKTRR***TISIFHRTRPPTGRLFFAWRRA*INAGEPRQERKGRGVALQNPWNLLWETVFDYS
LTNIQMGPKQATLRSSKTSRTYGTHCGTGQIGNSLHFRNQGCMP*GQ
>H8V34IS02FU9GO_rframe1
SDACNALTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKNTKMLIDYFHIPPDEAAHWALVLCMAPGVNKRRGTQKSRTEGGGALCVAKPIELAMSDGF
DYSLTNAQMGLKTGDPTQFKDFEDVWNAFVEQLKFGVALHFRNRDVCRRAEIR
>H8V34IS02FTRDI_rframe3
GRVQRSDRRHTRSILEYQNAGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHDEKNT
KMMIDYFNIPPDEAAHWALVLCMAPGVNKRRGTQKSRTEGGGGFCVGKPMELAMGDGFD
YSLTNTQIGPKTGDPTQFNSFEDVWNAFEEQVKFAAALHFRNRDVCRRAEIKY*

ideally, I get a fasta file containing the selected sequences.
Cheers, Marion.




Quote:
Originally Posted by MadeInGermany
Have you tried
Code:
grep "FDCIR" file

?
Multiple matches:
Code:
grep -e "FDCIR" -e "ALSNG" file

or
Code:
grep "\
FDCIR
ALSNG" file

or
Code:
egrep "FDCIR|ALSNG" file


Moderator's Comments:
Mod Comment Please use code tags next time for your code and data. Thanks


---------- Post updated at 04:19 AM ---------- Previous update was at 03:47 AM ----------

Hi
Thank you for the quick reply.
I did not work, the new file is empty.

Any other suggestions?
Cheers, Marion.


Quote:
Originally Posted by jim mcnamara
Code:
#  Try awk (or nawk on Solaris)
awk ' />/ {arr[$0]=""; i=$0; next}
        {arr[i]=arr[i] $0}
        END {for( p in arr) { if ( index(arr[p], "FCDIR")>0 ) {print p, arr[p] }}}
       '   fasta_file > newfile

 

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